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Publications (10 of 33) Show all publications
Naschberger, A., Fadeeva, M., Klaiman, D., Borovikova-Sheinker, A., Caspy, I., Nelson, N. & Amunts, A. (2024). Structure of plant photosystem I in a native assembly state defines PsaF as a regulatory checkpoint. Nature plants
Open this publication in new window or tab >>Structure of plant photosystem I in a native assembly state defines PsaF as a regulatory checkpoint
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2024 (English)In: Nature plants, ISSN 2055-026XArticle in journal (Refereed) Epub ahead of print
Abstract [en]

Plant photosystem I (PSI) consists of at least 13 nuclear-encoded and 4 chloroplast-encoded subunits that together act as a sunlight-driven oxidoreductase. Here we report the structure of a PSI assembly intermediate that we isolated from greening oat seedlings. The assembly intermediate shows an absence of at least eight subunits, including PsaF and LHCI, and lacks photoreduction activity. The data show that PsaF is a regulatory checkpoint that promotes the assembly of LHCI, effectively coupling biogenesis to function. This study reports the structure of a photosystem I assembly intermediate isolated from greening oat seedlings. It defines PsaF as a regulatory checkpoint promoting the association of LHCI that couples biogenesis to function.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-231205 (URN)10.1038/s41477-024-01699-8 (DOI)001235506400001 ()38816499 (PubMedID)2-s2.0-85194722138 (Scopus ID)
Available from: 2024-06-18 Created: 2024-06-18 Last updated: 2024-06-18
Mühleip, A., Kock Flygaard, R., Baradaran, R., Haapanen, O., Gruhl, T., Tobiasson, V., . . . Amunts, A. (2023). Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex. Nature, 615(7954), 934-938
Open this publication in new window or tab >>Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex
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2023 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 615, no 7954, p. 934-938Article in journal (Refereed) Published
Abstract [en]

Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I–II–III2–IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization

National Category
Biophysics
Identifiers
urn:nbn:se:su:diva-217000 (URN)10.1038/s41586-023-05817-y (DOI)000957757400002 ()36949187 (PubMedID)2-s2.0-85150748874 (Scopus ID)
Available from: 2023-05-23 Created: 2023-05-23 Last updated: 2023-05-24Bibliographically approved
Naschberger, A., Mosebach, L., Tobiasson, V., Kuhlgert, S., Scholz, M., Perez Boerema, A., . . . Amunts, A. (2022). Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex. Nature Plants, 8(10), 1191-1201
Open this publication in new window or tab >>Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex
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2022 (English)In: Nature Plants, ISSN 2055-0278, Vol. 8, no 10, p. 1191-1201Article in journal (Refereed) Published
Abstract [en]

Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Cryogenic electron microscopy identified that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI–light-harvesting complex I monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH and thus partially overlaps with the surface area that would bind one of the light-harvesting complex II complexes in state transitions. We also define the most accurate available PSI–light-harvesting complex I model at 2.3 Å resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations to all the pigments, as well as 621 water molecules that affect energy transfer pathways.

Keywords
plastocyanin, water, cyanobacterium, light harvesting system, metabolism, photosystem I, photosystem II, protein subunit, Cyanobacteria, Light-Harvesting Protein Complexes, Photosystem I Protein Complex, Photosystem II Protein Complex, Protein Subunits
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-211868 (URN)10.1038/s41477-022-01253-4 (DOI)000867562100001 ()36229605 (PubMedID)2-s2.0-85139980679 (Scopus ID)
Available from: 2022-11-29 Created: 2022-11-29 Last updated: 2022-11-29Bibliographically approved
Gahura, O., Mühleip, A., Hierro-Yap, C., Panicucci, B., Jain, M., Hollaus, D., . . . Amunts, A. (2022). An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases. Nature Communications, 13(1), Article ID 5989.
Open this publication in new window or tab >>An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases
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2022 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 5989Article in journal (Refereed) Published
Abstract [en]

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies. Mitochondrial ATP synthase assemble into oligomers. Here, authors resolve the structure of trypanosomal ATP synthase, showing that its dimerization is essential for function and evolutionary conserved.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-211078 (URN)10.1038/s41467-022-33588-z (DOI)000866124200004 ()36220811 (PubMedID)2-s2.0-85139627888 (Scopus ID)
Available from: 2022-11-10 Created: 2022-11-10 Last updated: 2023-03-28Bibliographically approved
Cottilli, P., Itoh, Y., Nobe, Y., Petrov, A. S., Lisón, P., Taoka, M. & Amunts, A. (2022). Cryo-EM structure and rRNA modification sites of a plant ribosome. Plant Communications, 3(5), Article ID 100342.
Open this publication in new window or tab >>Cryo-EM structure and rRNA modification sites of a plant ribosome
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2022 (English)In: Plant Communications, ISSN 2590-3462, Vol. 3, no 5, article id 100342Article in journal (Refereed) Published
Abstract [en]

Protein synthesis in crop plants contributes to the balance of food and fuel on our planet, which influences human metabolic activity and lifespan. Protein synthesis can be regulated with respect to changing environmental cues via the deposition of chemical modifications into rRNA. Here, we present the structure of a plant ribosome from tomato and a quantitative mass spectrometry analysis of its rRNAs. The study reveals fine features of the ribosomal proteins and 71 plant-specific rRNA modifications, and it re-annotates 30 rRNA residues in the available sequence. At the protein level, isoAsp is found in position 137 of uS11, and a zinc finger previously believed to be universal is missing from eL34, suggesting a lower effect of zinc deficiency on protein synthesis in plants. At the rRNA level, the plant ribosome differs markedly from its human counterpart with respect to the spatial distribution of modifications. Thus, it represents an additional layer of gene expression regulation, highlighting the molecular signature of a plant ribosome. The results provide a reference model of a plant ribosome for structural studies and an accurate marker for molecular ecology.

Keywords
plant, tomato, ribosome, RNA, structure
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-211926 (URN)10.1016/j.xplc.2022.100342 (DOI)000886977700012 ()35643637 (PubMedID)2-s2.0-85132763034 (Scopus ID)
Available from: 2022-12-01 Created: 2022-12-01 Last updated: 2022-12-06Bibliographically approved
Itoh, Y., Khawaja, A., Laptev, I., Cipullo, M., Atanassov, I., Sergiev, P., . . . Amunts, A. (2022). Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature, 606, 603-608
Open this publication in new window or tab >>Mechanism of mitoribosomal small subunit biogenesis and preinitiation
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2022 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 606, p. 603-608Article in journal (Refereed) Published
Abstract [en]

Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU–mS37–mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:su:diva-207051 (URN)10.1038/s41586-022-04795-x (DOI)000807992000002 ()35676484 (PubMedID)2-s2.0-85131571218 (Scopus ID)
Available from: 2022-07-05 Created: 2022-07-05 Last updated: 2022-07-05Bibliographically approved
Tobiasson, V., Berzina, I. & Amunts, A. (2022). Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements. Nature Communications, 13(1), Article ID 6132.
Open this publication in new window or tab >>Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements
2022 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 6132Article in journal (Refereed) Published
Abstract [en]

Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 angstrom resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-211075 (URN)10.1038/s41467-022-33582-5 (DOI)000871026900029 ()36253367 (PubMedID)2-s2.0-85132736023 (Scopus ID)
Available from: 2022-11-10 Created: 2022-11-10 Last updated: 2023-03-28Bibliographically approved
Itoh, Y., Singh, V., Khawaja, A., Naschberger, A., Nguyen, M. D., Rorbach, J. & Amunts, A. (2022). Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. eLIFE, 11, Article ID e77460.
Open this publication in new window or tab >>Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules
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2022 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 11, article id e77460Article in journal (Refereed) Published
Abstract [en]

The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron–sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron–sulfur, and the finding of iron–sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-213372 (URN)10.7554/eLife.77460 (DOI)000895763900001 ()36480258 (PubMedID)2-s2.0-85143564523 (Scopus ID)
Available from: 2023-01-09 Created: 2023-01-09 Last updated: 2023-03-16Bibliographically approved
Amunts, A. (2022). The revolution evolution. Nature Plants, 8(1), 14-17
Open this publication in new window or tab >>The revolution evolution
2022 (English)In: Nature Plants, ISSN 2055-0278, Vol. 8, no 1, p. 14-17Article in journal, Editorial material (Other academic) Published
Keywords
evolution, Biological Evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-209854 (URN)10.1038/s41477-021-01050-5 (DOI)000730891800002 ()34916598 (PubMedID)2-s2.0-85121453653 (Scopus ID)
Available from: 2022-09-28 Created: 2022-09-28 Last updated: 2022-09-28Bibliographically approved
Mühleip, A., Flygaard, R. K., Ovciarikova, J., Lacombe, A., Fernandes, P., Sheiner, L. & Amunts, A. (2021). ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria. Nature Communications, 12(1), Article ID 120.
Open this publication in new window or tab >>ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria
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2021 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 120Article in journal (Refereed) Published
Abstract [en]

Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF1. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-191723 (URN)10.1038/s41467-020-20381-z (DOI)000610428500004 ()33402698 (PubMedID)2-s2.0-85098749205 (Scopus ID)
Available from: 2021-03-31 Created: 2021-03-31 Last updated: 2023-10-24Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-5302-1740

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